The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

No Evidence for Recent Selection at FOXP2 among Diverse Human Populations.

FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.

Women's subsistence strategies predict fertility across cultures, but context matters.

While it is commonly assumed that farmers have higher, and foragers lower, fertility compared to populations practicing other forms of subsistence, robust supportive evidence is lacking. We tested whether subsistence activities-incorporating market integration-are associated with fertility in 10,250 women from 27 small-scale societies and found considerable variation in fertility. This variation did not align with group-level subsistence typologies. Societies labeled as "farmers" did not have higher fertility than others, while "foragers" did not have lower fertility. However, at the individual level, we found strong evidence that fertility was positively associated with farming and moderate evidence of a negative relationship between foraging and fertility. Markers of market integration were strongly negatively correlated with fertility. Despite strong cross-cultural evidence, these relationships were not consistent in all populations, highlighting the importance of the socioecological context, which likely influences the diverse mechanisms driving the relationship between fertility and subsistence.

Leveraging eco-evolutionary models for gene drive risk assessment.

Engineered gene drives create potential for both widespread benefits and irreversible harms to ecosystems. CRISPR-based systems of allelic conversion have rapidly accelerated gene drive research across diverse taxa, putting field trials and their necessary risk assessments on the horizon. Dynamic process-based models provide flexible quantitative platforms to predict gene drive outcomes in the context of system-specific ecological and evolutionary features. Here, we synthesize gene drive dynamic modeling studies to highlight research trends, knowledge gaps, and emergent principles, organized around their genetic, demographic, spatial, environmental, and implementation features. We identify the phenomena that most significantly influence model predictions, discuss limitations of biological complexity and uncertainty, and provide insights to promote responsible development and model-assisted risk assessment of gene drives.

Demographic rates reveal the benefits of protected areas in a long-lived migratory bird.

Recent studies have suggested that protected areas often fail to conserve target species. However, the efficacy of terrestrial protected areas is difficult to measure, especially for highly vagile species like migratory birds that may move between protected and unprotected areas throughout their lives. Here, we use a 30-y dataset of detailed demographic data from a migratory waterbird, the Whooper swan (Cygnus cygnus), to assess the value of nature reserves (NRs). We assess how demographic rates vary at sites with varying levels of protection and how they are influenced by movements between sites. Swans had a lower breeding probability when wintering inside NRs than outside but better survival for all age classes, generating a 30-fold higher annual growth rate within NRs. There was also a net movement of individuals from NRs to non-NRs. By combining these demographic rates and estimates of movement (into and out of NRs) into population projection models, we show that the NRs should help to double the population of swans wintering in the United Kingdom by 2030. These results highlight the major effect that spatial management can have on species conservation, even when the areas protected are relatively small and only used during short periods of the life cycle.

Variability in excess deaths across countries with different vulnerability during 2020-2023.

Excess deaths provide total impact estimates of major crises, such as the COVID-19 pandemic. We evaluated excess death trajectories across countries with accurate death registration and population age structure data and assessed relationships with vulnerability indicators. Using the Human Mortality Database on 34 countries, excess deaths were calculated for 2020-2023 (to week 29, 2023) using 2017-2019 as reference, with adjustment for 5 age strata. Countries were divided into less and more vulnerable; the latter had per capita nominal GDP < $30,000, Gini > 0.35 for income inequality and/or at least ≥2.5% of their population living in poverty. Excess deaths (as proportion of expected deaths, p%) were inversely correlated with per capita GDP (r = -0.60), correlated with proportion living in poverty (r = 0.66), and modestly correlated with income inequality (r = 0.45). Incidence rate ratio for deaths was 1.062 (95% CI, 1.038-1.087) in more versus less vulnerable countries. Excess deaths started deviating in the two groups after the first wave. Between-country heterogeneity diminished gradually within each group. Less vulnerable countries had mean p% = -0.8% and 0.4% in 0-64 and >65-y-old strata. More vulnerable countries had mean p% = 7.0% and 7.2%, respectively. Lower death rates were seen in children of age 0-14 y during 2020-2023 versus prepandemic years. While the pandemic hit some countries earlier than others, country vulnerability dominated eventually the cumulative impact. Half the analyzed countries witnessed no substantial excess deaths versus prepandemic levels, while the others suffered major death tolls.

Climate change, tree demography, and thermophilization in western US forests.

Climate change is driving widespread changes in ecological communities. Warming temperatures often shift community composition toward more heat-tolerant taxa. The factors influencing the rate of this "thermophilization" process remain unclear. Using 10-y census data from an extensive forest plot network, we show that mature tree communities of the western United States have undergone thermophilization. The mean magnitude of climate warming over the 10-y study interval was 0.32 °C, whereas the mean magnitude of thermophilization was 0.039 °C. Differential tree mortality was the strongest demographic driver of thermophilization, rather than growth or recruitment. Thermophilization rates are associated with recent changes in temperature and hydrologic variables, as well as topography and disturbance, with insect damage showing the strongest standardized effect on thermophilization rates. On average, thermophilization occurred more rapidly on cool, north-facing hillslopes. Our results demonstrate that warming temperatures are outpacing the composition of western US forest tree communities, and that climate change may erode biodiversity patterns structured by topographic variation.

Demographic consequences of phenological asynchrony for North American songbirds.

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Destabilizing effect of climate change on the persistence of a short-lived primate.

Seasonal tropical environments are among those regions that are the most affected by shifts in temperature and rainfall regimes under climate change, with potentially severe consequences for wildlife population persistence. This persistence is ultimately determined by complex demographic responses to multiple climatic drivers, yet these complexities have been little explored in tropical mammals. We use long-term, individual-based demographic data (1994 to 2020) from a short-lived primate in western Madagascar, the gray mouse lemur (Microcebus murinus), to investigate the demographic drivers of population persistence under observed shifts in seasonal temperature and rainfall. While rainfall during the wet season has been declining over the years, dry season temperatures have been increasing, with these trends projected to continue. These environmental changes resulted in lower survival and higher recruitment rates over time for gray mouse lemurs. Although the contrasting changes have prevented the study population from collapsing, the resulting increase in life-history speed has destabilized an otherwise stable population. Population projections under more recent rainfall and temperature levels predict an increase in population fluctuations and a corresponding increase in the extinction risk over the next five decades. Our analyses show that a relatively short-lived mammal with high reproductive output, representing a life history that is expected to closely track changes in its environment, can nonetheless be threatened by climate change.

Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist.

The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.

Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot.

Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.

More comprehensive sex education reduced teen births: Quasi-experimental evidence.

Women in the United States are much more likely to become mothers as teens than those in other rich countries. Teen births are particularly likely to be reported as unintended, leading to debate over whether better information on sex and contraception might lead to reductions in teen births. We contribute to this debate by providing causal evidence at the population level. Our causal identification strategy exploits county-level variation in the timing and receipt of federal funding for more comprehensive sex education and data on age-specific teen birth rates at the county level constructed from birth certificate natality data covering all births in the United States. Our results show that federal funding for more comprehensive sex education reduced county-level teen birth rates by more than 3%. Our findings thus complement the mixed evidence to date from randomized control trials on teen pregnancies and births by providing population-level causal evidence that federal funding for more comprehensive sex education led to reductions in teen births.

Female reproductive aging in seven primate species: Patterns and consequences.

Age-related changes in fertility have increasingly been documented in wild animal populations: In many species the youngest and oldest reproducers are disadvantaged relative to prime adults. How do these effects evolve, and what explains their diversity across species? Tackling this question requires detailed data on patterns of age-related reproductive performance in multiple animal species. Here, we compare patterns and consequences of age-related changes in female reproductive performance in seven primate populations that have been subjects of long-term continuous study for 29 to 57 y. We document evidence of age effects on fertility and on offspring performance in most, but not all, of these primate species. Specifically, females of six species showed longer interbirth intervals in the oldest age classes, youngest age classes, or both, and the oldest females also showed relatively fewer completed interbirth intervals. In addition, five species showed markedly lower survival among offspring born to the oldest mothers, and two species showed reduced survival for offspring born to both the youngest and the oldest mothers. In contrast, we found mixed evidence that maternal age affects the age at which daughters first reproduce: Only in muriquis and to some extent in chimpanzees, the only two species with female-biased dispersal, did relatively young mothers produce daughters that tended to have earlier first reproduction. Our findings demonstrate shared patterns as well as contrasts in age-related changes in female fertility across species of nonhuman primates and highlight species-specific behavior and life-history patterns as possible explanations for species-level differences.

Estimating bonobo (Panpaniscus) and chimpanzee (Pantroglodytes) evolutionary history from nucleotide site patterns.

Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models. Here, we investigate this gap in knowledge using nucleotide site patterns calculated from whole-genome sequences from the autosomes of 71 bonobos and chimpanzees, representing all five extant Pan lineages. We estimated demographic parameters and compared all previously proposed demographic models for this clade. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. We show that 1) 21% of autosomal DNA in eastern chimpanzees derives from western chimpanzee introgression and that 2) all four chimpanzee lineages share a common ancestor about 987,000 y ago, much earlier than previous estimates. In addition, we suggest that 3) there was male reproductive skew throughout Pan evolutionary history and find evidence of 4) male-biased dispersal from western to eastern chimpanzees. Collectively, these results offer insight into bonobo and chimpanzee evolutionary history and suggest considerable differences between current and historic chimpanzee biogeography.

Assessing the role of multiple mechanisms increasing the age of dengue cases in Thailand.

The mean age of dengue hemorrhagic fever (DHF) cases increased considerably in Thailand from 8.1 to 24.3 y between 1981 and 2017 (mean annual increase of 0.45 y). Alternative proposed explanations for this trend, such as changes in surveillance practices, reduced mosquito­human contact, and shifts in population demographics, have different implications for global dengue epidemiology. To evaluate the contribution of each of these hypothesized mechanisms to the observed data, we developed 20 nested epidemiological models of dengue virus infection, allowing for variation over time in population demographics, infection hazards, and reporting rates. We also quantified the effect of removing or retaining each source of variation in simulations of the age trajectory. Shifts in the age structure of susceptibility explained 58% of the observed change in age. Adding heterogeneous reporting by age and reductions in per-serotype infection hazard to models with shifts in susceptibility explained an additional 42%. Reductions in infection hazards were mostly driven by changes in the number of infectious individuals at any time (another consequence of shifting age demographics) rather than changes in the transmissibility of individual infections. We conclude that the demographic transition drives the overwhelming majority of the observed change as it changes both the age structure of susceptibility and the number of infectious individuals. With the projected Thai population age structure, our results suggest a continuing increase in age of DHF cases, shifting the burden toward individuals with more comorbidity. These insights into dengue epidemiology may be relevant to many regions of the globe currently undergoing comparable changes in population demographics.

Significant impacts of the COVID-19 pandemic on race/ethnic differences in US mortality.

The coronavirus 2019 (COVID-19) pandemic triggered global declines in life expectancy. The United States was hit particularly hard among high-income countries. Early data from the United States showed that these losses varied greatly by race/ethnicity in 2020, with Hispanic and Black Americans suffering much larger losses in life expectancy compared with White people. We add to this research by examining trends in lifespan inequality, average years of life lost, and the contribution of specific causes of death and ages to race/ethnic life-expectancy disparities in the United States from 2010 to 2020. We find that life expectancy in 2020 fell more for Hispanic and Black males (4.5 and 3.6 y, respectively) compared with White males (1.5 y). These drops nearly eliminated the previous life-expectancy advantage for the Hispanic compared with the White population, while dramatically increasing the already large gap in life expectancy between Black and White people. While the drops in life expectancy for the Hispanic population were largely attributable to official COVID-19 deaths, Black Americans saw increases in cardiovascular diseases and "deaths of despair" over this period. In 2020, lifespan inequality increased slightly for Hispanic and White populations but decreased for Black people, reflecting the younger age pattern of COVID-19 deaths for Hispanic people. Overall, the mortality burden of the COVID-19 pandemic hit race/ethnic minorities particularly hard in the United States, underscoring the importance of the social determinants of health during a public health crisis.

Incidence and Outcomes of Cardiocerebral Infarction: A Cohort Study of 2 National Population-Based Registries.

BACKGROUND: Cardiocerebral infarction (CCI), which is concomitant with acute myocardial infarction (AMI) and acute ischemic stroke (AIS), is a rare but severe presentation. However, there are few data on CCI, and the treatment options are uncertain. We investigated the characteristics and outcomes of CCI compared with AMI or AIS alone. METHODS: We performed a retrospective cohort study of 120 531 patients with AMI and AIS from the national stroke and AMI registries in Singapore. Patients were categorized into AMI only, AIS only, synchronous CCI (same-day), and metachronous CCI (within 1 week). The primary outcome was all-cause mortality, and the secondary outcome was cardiovascular mortality. The mortality risks were compared using Cox regression. Multivariable models were adjusted for baseline demographics, clinical variables, and treatment for AMI or AIS. RESULTS: Of 127 919 patients identified, 120 531 (94.2%) were included; 74 219 (61.6%) patients had AMI only, 44 721 (37.1%) had AIS only, 625 (0.5%) had synchronous CCI, and 966 (0.8%) had metachronous CCI. The mean age was 67.7 (SD, 14.0) years. Synchronous and metachronous CCI had a higher risk of 30-day mortality (synchronous: adjusted HR [aHR], 2.41 [95% CI, 1.77-3.28]; metachronous: aHR, 2.80 [95% CI, 2.11-3.73]) than AMI only and AIS only (synchronous: aHR, 2.90 [95% CI, 1.87-4.51]; metachronous: aHR, 4.36 [95% CI, 3.03-6.27]). The risk of cardiovascular mortality was higher in synchronous and metachronous CCI than AMI (synchronous: aHR, 3.03 [95% CI, 2.15-4.28]; metachronous: aHR, 3.41 [95% CI, 2.50-4.65]) or AIS only (synchronous: aHR, 2.58 [95% CI, 1.52-4.36]; metachronous: aHR, 4.52 [95% CI, 2.95-6.92]). In synchronous CCI, AMI was less likely to be managed with PCI and secondary prevention medications (P<0.001) compared with AMI only. CONCLUSIONS: Synchronous CCI occurred in 1 in 200 cases of AIS and AMI. Synchronous and metachronous CCI had higher mortality than AMI or AIS alone.

Epidemiology, Pathophysiology, and Imaging of Atherosclerotic Intracranial Disease.

Intracranial atherosclerotic disease (ICAD) is one of the most common causes of stroke worldwide. Among people with stroke, those of East Asia descent and non-White populations in the United States have a higher burden of ICAD-related stroke compared with Whites of European descent. Disparities in the prevalence of asymptomatic ICAD are less marked than with symptomatic ICAD. In addition to stroke, ICAD increases the risk of dementia and cognitive decline, magnifying ICAD societal burden. The risk of stroke recurrence among patients with ICAD-related stroke is the highest among those with confirmed stroke and stenosis ≥70%. In fact, the 1-year recurrent stroke rate of >20% among those with stenosis >70% is one of the highest rates among common causes of stroke. The mechanisms by which ICAD causes stroke include plaque rupture with in situ thrombosis and occlusion or artery-to-artery embolization, hemodynamic injury, and branch occlusive disease. The risk of stroke recurrence varies by the presumed underlying mechanism of stroke, but whether techniques such as quantitative magnetic resonance angiography, computed tomographic angiography, magnetic resonance perfusion, or transcranial Doppler can help with risk stratification beyond the degree of stenosis is less clear. The diagnosis of ICAD is heavily reliant on lumen-based studies, such as computed tomographic angiography, magnetic resonance angiography, or digital subtraction angiography, but newer technologies, such as high-resolution vessel wall magnetic resonance imaging, can help distinguish ICAD from stenosing arteriopathies.

Natural recovery of corals after severe disturbance.

Ecosystem recovery from human-induced disturbances, whether through natural processes or restoration, is occurring worldwide. Yet, recovery dynamics, and their implications for broader ecosystem management, remain unclear. We explored recovery dynamics using coral reefs as a case study. We tracked the fate of 809 individual coral recruits that settled after a severe bleaching event at Lizard Island, Great Barrier Reef. Recruited Acropora corals, first detected in 2020, grew to coral cover levels that were equivalent to global average coral cover within just 2 years. Furthermore, we found that just 11.5 Acropora recruits per square meter were sufficient to reach this cover within 2 years. However, wave exposure, growth form and colony density had a marked effect on recovery rates. Our results underscore the importance of considering natural recovery in management and restoration and highlight how lessons learnt from reef recovery can inform our understanding of recovery dynamics in high-diversity climate-disturbed ecosystems.

Reconstructing 120 years of climate change impacts on Joshua tree flowering.

Quantifying how global change impacts wild populations remains challenging, especially for species poorly represented by systematic datasets. Here, we infer climate change effects on masting by Joshua trees (Yucca brevifolia and Y. jaegeriana), keystone perennials of the Mojave Desert, from 15 years of crowdsourced observations. We annotated phenophase in 10,212 geo-referenced images of Joshua trees on the iNaturalist crowdsourcing platform, and used them to train machine learning models predicting flowering from annual weather records. Hindcasting to 1900 with a trained model successfully recovers flowering events in independent historical records and reveals a slightly rising frequency of conditions supporting flowering since the early 20th Century. This reflects increased variation in annual precipitation, which drives masting events in wet years-but also increasing temperatures and drought stress, which may have net negative impacts on recruitment. Our findings reaffirm the value of crowdsourcing for understanding climate change impacts on biodiversity.